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Nina Chatterjee, Rupal Ojha, Nazia Khatoon, Vijay Kumar Prajapati
Tuberculosis is a menacing disease caused eminently to the people inhabiting the tropical and sub-tropical nations. A holistic approach is required to generate T and B memory cells to effectuate a long-term exemption from the pulmonary tuberculosis. In this study, immunoinformatic approaches were used to design a multi-epitope-based subunit vaccine for pulmonary tuberculosis which may improve human immune system. The various B-cell, TH cell and TC cell binding epitopes were predicted for selected 2 membrane and 12 secretory proteins of Mycobacterium tuberculosis...
June 16, 2018: International Journal of Biological Macromolecules
Monica A Thomas, Jie He, Francis C Peterson, Anna R Huppler, Brian F Volkman
The chemokine CCL28 is constitutively expressed in mucosal tissues and is abundant in low-salt mucosal secretions. Beyond its traditional role as a chemoattractant, CCL28 has been shown to act as a potent and broad-spectrum antimicrobial agent with particular efficacy against the commensal fungus and opportunistic pathogen Candida albicans. However, the structural features that allow CCL28 to perform its chemotactic and antimicrobial functions remain unknown. Here, we report the structure of CCL28, solved using nuclear magnetic resonance spectroscopy...
June 15, 2018: Journal of Molecular Biology
Georg Mohr, Sean Yoon-Seo Kang, Seung Kuk Park, Yidan Qin, Jacob Grohman, Jun Yao, Jennifer L Stamos, Alan M Lambowitz
The thermostable Geobacillus stearothermophilus GsI-IIC intron is among the few bacterial group II introns found to proliferate to high copy number in its host genome. Here, we developed a bacterial genetic assay for retrohoming and biochemical assays for protein-dependent and self-splicing of GsI-IIC. We found that GsI-IIC, like other group IIC introns, retrohomes into sites having a 5'-exon DNA hairpin, typically from a bacterial transcription terminator, followed by short intron-binding sequences (IBSs) recognized by base pairing of exon-binding sequences (EBSs) in the intron RNA...
June 15, 2018: Journal of Molecular Biology
Zishuo Cheng, Pei W Thomas, Lincheng Ju, Alexander Bergstrom, Kelly Mason, Delaney Clayton, Callie Miller, Christopher R Bethel, Jamie VanPelt, David L Tierney, Richard C Page, Robert A Bonomo, Walter Fast, Michael W Crowder
Infections by carbapenem-resistant Enterobacteriaceae (CRE) are difficult to manage owing to broad antibiotic resistance profiles and because of the inability of clinically-used β-lactamase inhibitors to counter the activity of metallo-β-lactamases often harbored by these pathogens. Of particular importance is New Delhi metallo-β-lactamase (NDM), which requires a dinuclear zinc ion cluster for catalytic activity. Here, we compare the structures and functions of clinical NDM variants 1-17. The impact of NDM variants on structure is probed by comparing comparing melting temperature and refolding efficiency and also by spectroscopy (UV-Vis, 1 H-NMR, and EPR) of di-cobalt metalloforms...
June 16, 2018: Journal of Biological Chemistry
V R Coluci, S O Dantas, V K Tewary
The need of small integration time steps (∼1 fs) in conventional molecular dynamics simulations is an important issue that inhibits the study of physical, chemical, and biological systems in real timescales. Additionally, to simulate those systems in contact with a thermal bath, thermostating techniques are usually applied. In this work, we generalize the Green's function molecular dynamics technique to allow simulations within the canonical ensemble. By applying this technique to one-dimensional systems, we were able to correctly describe important thermodynamic properties such as the temperature fluctuations, the temperature distribution, and the velocity autocorrelation function...
May 2018: Physical Review. E
Arzu Coleri Cihan, Emine Derebay Yildiz, Ergin Sahin, Ozal Mutlu
Among the thermophilic Bacillaceae family members, α-amylase production of 15 bacilli from genus Anoxybacillus was investigated, some of which are biotechnologically important. These Anoxybacillus α-amylase genes displayed ≥ 91.0% sequence similarities to Anoxybacillus enzymes (ASKA, ADTA and GSX-BL), but relatively lower similarities to Geobacillus (≤ 69.4% to GTA, Gt-amyII), and Bacillus aquimaris (≤ 61.3% to BaqA) amylases, all formerly proposed only in a Glycoside Hydrolase 13 (GH13) subfamily...
June 15, 2018: World Journal of Microbiology & Biotechnology
Poulomi Saha, Mohd Faheem Khan, Sanjukta Patra
Enzymes are indispensable biocatalysts required in various steps of textile processing to minimize various chemical-induced hazards. The present work focuses on the applications of the truncated α-amylase in textile industry for desizing of fabrics by starch hydrolysis. The multiple sequence alignment was performed to find homology and the possible truncation region in Bacillus subtilis MTCC 121 α-amylase with same bacilli family α-amylase. Two constructs were generated for α-amylase gene of Bacillus subtilis MTCC 121 (Amy_F, full-length and Amy_T, C-terminal truncated) were cloned, overexpressed, purified, and characterized...
June 14, 2018: Preparative Biochemistry & Biotechnology
Xuejia Shi, Linguo Zhao, Jianjun Pei, Lin Ge, Pengwei Wan, Zhenzhong Wang, Wei Xiao
In this article, the methods for detection of enzyme activity and protein concentration are described. The data of the calibration curves can be used for a further understanding on the assays of enzyme activity measured with p -nitrophenyl-β-D-glucopyranoside ( p NPG) or cellobiose as the substrate. In addition, the data presented provides an analytic method for measuring protein concentration in mixed samples.
June 2018: Data in Brief
Daniel H Lin, Ana R Correia, Sarah W Cai, Ferdinand M Huber, Claudia A Jette, André Hoelz
The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1•Nxt1 from mRNAs. Here, we report crystal structures of Gle1•Nup42 from three organisms that reveal an evolutionarily conserved binding mode. Biochemical reconstitution of the DDX19 ATPase cycle establishes that human DDX19 activation does not require IP6 , unlike its fungal homologs, and that Gle1 stability affects DDX19 activation...
June 13, 2018: Nature Communications
Susanne Bury, Manonmani Soundararajan, Richa Bharti, Rudolf von Bünau, Konrad U Förstner, Tobias A Oelschlaeger
Shiga toxin (Stx) producing E. coli (STEC) such as Enterohemorrhagic E. coli (EHEC) are the major cause of foodborne illness in humans. In vitro studies showed the probiotic Escherichia coli strain Nissle 1917 (EcN) to efficiently inhibit the production of Stx. Life threatening EHEC strains as for example the serotype O104:H4, responsible for the great outbreak in 2011 in Germany, evolutionary developed from certain E. coli strains which got infected by stx2 -encoding lambdoid phages turning the E. coli into lysogenic and subsequently Stx producing strains...
2018: Frontiers in Microbiology
Sai-Sai Li, Yan Li, Neng-Bing Long, Feng Jiang, Rui-Feng Zhang
Phospholipase D (PLD) was effectively immobilized on a ZnO nanowires/macroporous SiO2 composite support through an in-situ cross-linking method. An anionic and long-chained bi-epoxy cross-linker was used by adsorbing on the surface of ZnO nanowires through static interaction before cross-linking. Under the fine control of in-situ cross-linking the immobilized PLD has loading amount as high as 113.7 mg/gsupport , possessing high specific activity from 13,987 to 16,142 U/gprotein in all the range of loading amount...
June 9, 2018: International Journal of Biological Macromolecules
Seaim Lwin Aye, Kei Fujiwara, Nobuhide Doi
Engineering and design of genetic circuit in living cell is critical in accessing the beneficial application of synthetic biology. Directed evolution can avoid the complicated rational design of such circuit by screening or selecting functional circuit from non-functional one. Here we proposed a positive-negative selection system for selecting a transcription factor that activates gene expression in response to arsenic in solution. First, we developed a whole cell biosensor for sensing arsenite in liquid using a regulator (ArsR) and a reporter (GFP), and evaluated its performance...
June 8, 2018: Journal of Biochemistry
Xiaolong Wang, Jingnü Xian, Gang Chen, Haibo Peng
Oligonucleotides are widely used as effective tools to regulate gene expression and drugs for targeted gene therapy. Therefore, they are potentially useful for the treatment of viral, tumor and hereditary diseases. Therapeutic oligonucleotides include antisense oligonucleotide, small interference RNA (siRNA), Ribozyme, DNAzyme, anti-gene, CpG, decoy and aptamer. Therapeutic oligonucleotides usually carry certain modifications, such as phosphorothioates, fluoro or locked nucleic acids, to enhance the stability and specificity, and reduce the side-effects, because natural oligonucleotides have poor stability in vivo, low specificity and side effects...
May 25, 2018: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
Yogesh Kumar Negi, Chitra Pandey, Neha Saxena, Sonika Sharma, F C Garg, S K Garg
The study was aimed to isolate antagonistic lactobacilli and the molecules responsible for their antagonistic ability from curd. Preparation of probiotic curd and the ability of the selected lactobacilli to suppress the pathogen therein was also assessed. All the 116 isolates were identified as Lactobacillus spp. based on morphological, biochemical and curdling assays. Five of these lactobacilli (Lb-17, Lb-33, Lb-108, Lb-112, and Lb-N3) were found most promising to inhibit all test pathogens ( Staphylococcus aureus , Escherichia coli , Klebsiella pneumoniae , Salmonella typhi and Shigella sonnei )...
June 2018: Journal of Food Science and Technology
Norihisa Haraguchi, Jun Kaseda, Yasumune Nakayama, Kazuhiro Nagahama, Takahira Ogawa, Masayoshi Matsuoka
Photosystem II complex embedded in thylakoid membrane performs oxygenic photosynthesis where the reaction center D1/D2 heterodimer accommodates all components of the electron transport chain. To express thermostable D1/D2 heterodimer in a cyanobacterium Synechococcus elongatus PCC 7942, we constructed a series of mutant strains whose psbA1 and psbD1 genes encoding, respectively, the most highly expressed D1 and D2 polypeptides were replaced with those of a thermophilic strain, Thermosynechococcus vulcanus. Because the C-terminal 16 amino acid sequences of D1 polypeptides should be processed prior to maturation but diverge from each other, we also constructed the psbA1ΔC-replaced strain expressing a thermostable D1 polypeptide devoid of the C-terminal extension...
June 8, 2018: Journal of Bioscience and Bioengineering
Dattatray Bedade, Jan Deska, Sandip Bankar, Samir Bejar, Rekha Singhal, Salem Shamekh
Truffles are symbiotic hypogeous edible fungi (form of mushroom) that form filamentous mycelia in their initial phase of the growth cycle as well as a symbiotic association with host plant roots. In the present study, Tuber maculatum mycelia were isolated and tested for extracellular amylase production at different pH on solid agar medium. Furthermore, the mycelium was subjected to submerged fermentation for amylase production under different culture conditions such as variable carbon sources and their concentrations, initial medium pH, and incubation time...
June 11, 2018: Preparative Biochemistry & Biotechnology
Malwina Ewa Sosnowska, Urszula Jankiewicz, Marta Kutwin, André Chwalibog, Agnieszka Gałązka
Cells of Escherichia coli Rosetta, containing plasmid pET-28a with sequences of DNA of chitinase from Stenotrophomonas maltophilia N4, were used for the efficient synthesis of recombinant chitinolytic enzyme. The objective of this study was to improve thermal stability of the recombinant chitinase by salts and metal nanoparticles (NP). The studied chitinase was thermolabile and largely lost its activity in the first minutes of storage at 50 and 60 °C. The optimum temperature for colloidal chitin hydrolysis by the enzyme was 50 °C...
September 2018: Enzyme and Microbial Technology
Maria Bawn, Fabiana Subrizi, Gary J Lye, Tom D Sheppard, Helen C Hailes, John M Ward
The use of biocatalysis for the synthesis of high value added chemical building blocks derived from biomass is becoming an increasingly important application for future sustainable technologies. The synthesis of a higher value chemical from l-arabinose, the predominant monosaccharide obtained from sugar beet pulp, is demonstrated here via a transketolase and transaminase coupled reaction. Thermostable transketolases derived from Deinococcus geothermalis and Deinococcus radiodurans catalysed the synthesis of l-gluco-heptulose from l-arabinose and β-hydroxypyruvate at elevated temperatures with high conversions...
September 2018: Enzyme and Microbial Technology
Kavita Bhatia, Gorakh Mal, Rasbihari Bhar, Jyoti, Chandrika Attri, Amit Seth
A thermostable superoxide dismutase from thermophilic bacterium Anoxybacillus gonensis KA 55 MTCC 12684 which was isolated from Manikaran hotspring of Himachal Pradesh was purified to apparent homogeneity by fractional ammonium sulphate precipitation and anion exchange chromatography. A purification factor of 33.1-fold was achieved, with the purified enzyme exhibiting specific activity of 5758.4 U/mg protein. The purified superoxide dismutase was optimally active at pH 9.0 and displayed stability over a broad pH range of 7...
June 7, 2018: International Journal of Biological Macromolecules
Ichiro Hisaki, Yuto Suzuki, Eduardo Gomez, Boiko Cohen, Norimitsu Tohnai, Abderrazzak Douhal
Enhancement of thermal and chemical durability and an increase of surface area are two main directions for the construction and improvement of the performance of porous hydrogen-bonded organic frameworks (HOFs). Herein, we propose that a hexaazatriphenylene (HAT) derivative, which possesses six carboxyaryl groups, is a suitable building block for the systematic construction of thermally and chemically durable HOFs with large surface area due to shape-fitted docking between the HAT cores and interpenetrated three-dimensional network...
June 9, 2018: Angewandte Chemie
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